MuD Logo Annotating the affect of missense mutations on the
protein's function using sequence and structural features
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Mutation submission Format:

Quaternary structures selection

The prediction's accuracy is improved by supplying the prediction scheme with the structure of the biological unit of the protein. Hence, this stage of the prediction presents all the available quaternary structures of the protein as predicted by the PQS server(1). The structures are clustered according to the accessible surface area. You can chose to omit from the prediction scheme structures or specific chains and retain only the biological unit.

Ligand selection

Crystal structures often include ingredients of the crystallization solution. This stage in the prediction scheme allows you to guide the prediction scheme and remove biologically irrelevant ligands. Filtering out all the irrelevant ligands improves the prediction accuracy.

Sites of interest in the structure

The Swiss-Prot (2) annotations withhold information regarding positions that are importnat to the proteins function. This form presents these annotated positions and allows omission and addition of positions. The form presents amino acid(s) involved in the activity of an enzyme, binding site for any chemical group, glycosylation site, extent of a calcium-binding region, DNA-binding region, covalent binding of a lipid moiety, metal ion binding site, nucleotide phosphate-binding region, any interesting single amino-acid site on the sequence that is not defined by another feature key, extent of a zinc finger region, and redidues that undergo posttranslational modification.

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References

  1. Henrick, K. and Thornton, J.M. (1998) PQS: a protein quaternary structure file server. Trends in biochemical sciences, 23, 358-361.
  2. Boeckmann, B., Bairoch, A., Apweiler, R., Blatter, M.C., Estreicher, A., Gasteiger, E., Martin, M.J., Michoud, K., O'Donovan, C., Phan, I. et al. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res, 31, 365-370.